Was the Malaysian Airliner crash caused by a non-benign artificial intelligence system?
Short answer: despite the incredible advances in AI via Machine Learning (and subfields) AI is nowhere near this kind of autonomous decision-making.

I can't prove a negative, but, the level of autonomy Musk is talking about is still on the horizon.

Doesn't mean Musk is wrong about the hypothetical.  imo I'm glad he keeps bringing these kinds of issues to the fore.  

Engineers and mathematicians have a bit more credibility on this subject than laypeople.  If it seems alarmist, there are many in the scientific community who feel it is warranted.

What Musk is describing is an extension of what Asimov felt compelled to warn us about via his "Three Laws of Robotics" back in 1942, when computers sucked.  For an explication of this idea re: Machine Learning, see below.



JUST FOR FUN (SORT OF:)

Author and mathematical physicist Hannu Rajaniemi just published a story in the MIT Tech Review on this very subject.  

Unchained: A Story of Love, Loss, and Blockchain

Warning: the story is both wickedly funny, surprisingly moving, and very likely prescient!